Perhaps there was a curse or some dark magic at play. A curse that made the hunters see Percy as an enemy when he was actually an ally, leading to his untimely death.
One possible reason could be that hunters have been interfering in Percy's quests. If they show up uninvited and start taking over or causing chaos, Percy would get angry. For example, if they start hunting a monster that Percy has been tracking for a long time.
Maybe Percy unknowingly breaks some ancient and very strict laws of the Gods. For example, he might interfere with some sacred rituals or places that are off - limits to mortals, even demigods like him. In the fanfiction world, the Gods could be very unforgiving when it comes to such violations and decide to kill him as a result.
One possible theme could be the exploration of power dynamics. The hunters may be in a position of power over Percy, and the abuse could show how power can be misused. Another theme might be trauma and its aftermath. Percy would likely experience a great deal of emotional and physical trauma from the abuse, and the fanfiction could delve into how he copes or fails to cope.
Perhaps the hunters always interfere in Percy's adventures. They might show up at the wrong time and disrupt his plans. For instance, Percy was about to rescue someone, and the hunters came and took over, but in a way that put the person in more danger. This would make Percy resent them. Also, if the hunters have some internal politics that end up affecting Percy negatively, like they accuse him of something he didn't do just to protect their own reputation, that could lead to his hatred.
One possibility is that there is a prophecy that involves Percy and the hunters in a way that the hunters misinterpret. They believe that by torturing Percy, they can prevent some great disaster. However, Percy is actually an important part of the solution, not the problem. As the story progresses, he could start to communicate with some of the more sympathetic hunters and try to make them see the truth.
It could be because Percy is different. If he comes from a different background or has a unique personality trait, the bullies might target him. In the fanfiction, if Percy is from a different race or has an unusual way of speaking, the bullies might pick on him for not being like them.
Perhaps it's part of a grand plan that Poseidon has, one that he believes will ultimately benefit Percy but in the short - term causes him pain. For example, he might be trying to toughen Percy up or make him prove himself in a more extreme way, thinking it will help Percy in the long run.
It could be due to physical injury. Maybe he got hurt in a battle or an accident within the fictional world of the story.
It could also be that in the fanfiction, Percy is given a new power or ability that Annabeth sees as a threat. Or perhaps Percy is made to side with someone Annabeth dislikes, causing her to 'hate' him in that fan - created story. This shows how different plot elements in fanfiction can change the dynamics between characters.
Perhaps the fanfiction is set in an alternate universe where something has happened to change Percy's feelings towards Annabeth. For example, if there was a betrayal in the fan - created story that made Percy turn against her.